Metabolomics, the science that describes a full range of small molecules in a sample at a time point, is a powerful tool to evaluate patterns in metabolite variations affected by environmental factors. We developed a multiblock metabolomics approach using LC-HRMS, HS-SPME-GC–MS and 1H NMR to study the interspecies and temporal metabolites variations of two red algae species from the genus Asparagopsis well-known for their broad range of biological activities. Samples were collected over two years at 5 sites. For each sample, a biphasic extraction was performed to allow distinct analyses of apolar phases by LC-HRMS and of polar phases by 1H NMR. The remaining lyophilized algal powder was analysed using a HS-SPME-GC–MS method. Temporal variation of antibacterial activities of extracts of the two algae was also studied and its potential covariation with algal metabolome was evaluated. On the one hand, the multiblock analysis allowed the interspecies and temporal discrimination of the two species, and putative identification of potential chemotaxonomic markers including highly halogenated molecules. Organosulfur compounds enriched in A. armata samples could be detected with both 1H NMR (taurine and isethionic acid) and LC-HRMS (sulfolipids). On the other hand, the variation in several metabolites intensities could be related to temporal effects, probably linked to environmental factors. It is the case of floridoside, a major carbohydrate, and citrulline (1H NMR) that both can have antioxidant properties, but also of various sulfolipids (LC-HRMS). The antibacterial activity of extracts of both species was constant throughout the year and did not covary with metabolome. This work is also the first to report the study of the metabolome of the two different species of the genus Asparagopsis by 1H NMR and HS-SPME-GC–MS.